FunGen-xQTL Resources

Data catalog

Every dataset page in the catalog: QTL results, the omics data behind them, AD GWAS and reference data. Search and filters work together, and the web address keeps them, so a filtered view can be bookmarked or shared.

QTL results by cohort and modality

Number of QTL result pages. Select a cell, a cohort or a modality to filter the table.

Analysis progress by method

QTL result pages that record each method as done, out of 28. Hover a row for the datasets. Full coverage grid
  • cis-QTL 20 of 28
  • SuSiE 11 of 28
  • fSuSiE not recorded
  • ColocBoost 2 of 28
  • TWAS 10 of 28
  • cTWAS 6 of 28
  • MR not recorded
  • LF2 not recorded
  • scEEMS not recorded

Tissues and cell types per dataset

QTL datasets that cover more than one brain region or cell type. The other 22 cover one each.

QTL datasets by cohort

Share of the 28 QTL datasets that come from each cohort.
  • ROSMAP 16 57%
  • Knight-ADRC 5 18%
  • MSBB 4 14%
  • Other MetaBrain, MiGA, STARNET 3 11%
73 datasets
Datasets in the FunGen-xQTL catalog
Tissue / cellStatusAccessLocation
AD GWAS Summary StatisticsAD GWASGWAS—Stagedsyn69670651
ADGC GWAS imputation protocolAD GWASProtocol—StagedPublic URL
Alzheimer's Disease GWAS Summary Data (Bellenguez)AD GWASGWAS—Stagedsyn69670625
Alzheimer's Disease GWAS Summary Data (Jansen)AD GWASGWAS—Stagedsyn69670625
Alzheimer's Disease GWAS Summary Data (Kunkle)AD GWASGWAS—Stagedsyn69670625
Alzheimer's Disease GWAS Summary Data (Wightman)AD GWASGWAS—Stagedsyn69670625
FunGen-xQTL protocol dataROSMAPProtocol—Stagedsyn36416601
Knight ADRC brain gene expressionKnight-ADRCExpressionparietal cortex—StagedControlledsyn69670592
Knight ADRC brain gene expression QTLKnight-ADRCeQTLparietal cortex—StagedControlledsyn69670592
Knight ADRC brain metabolomicsKnight-ADRCMetabolomicsparietal cortex—StagedControlled—
Knight ADRC brain metabolomics QTLKnight-ADRCmetQTLparietal cortex—StagedControlled—
Knight ADRC brain methylationKnight-ADRCMethylationparietal cortex—StagedControlledsyn69670592
Knight ADRC brain methylation QTLKnight-ADRCmQTLparietal cortex—StagedControlledsyn69670592
Knight ADRC brain proteomicsKnight-ADRCProteomicsparietal cortex442StagedControlledsyn69670592
Knight ADRC brain proteomics QTLKnight-ADRCpQTLparietal cortex412StagedControlledsyn69670592
Knight ADRC brain splicingKnight-ADRCSplicingparietal cortex—StagedControlledsyn69670592
Knight ADRC brain splicing QTLKnight-ADRCsQTLparietal cortex—StagedControlledsyn69670592
Knight ADRC genotype dataKnight-ADRCGenotype / WGSblood—StagedControlled—
MetaBrain Brain ExpressionMetaBrainExpression5 brain regions—Stagedsyn69670592
MetaBrain Brain Gene Expression QTLMetaBraineQTL5 brain regions—Stagedsyn69670592
MiGA genotype dataMiGAGenotype / WGS—StagedControlled—
MiGA multi-brain region gene expressionMiGAExpressionmicroglia, 4 regions—StagedControlledsyn69670592
MiGA multi-brain region gene expressionMiGAeQTLmicroglia255StagedControlledsyn69670592
MSBB brain alternative splicingMSBBSplicing4 brain regions—StagedControlledsyn69670592
MSBB brain alternative splicing QTLMSBBsQTL4 brain regions—StagedControlledsyn69670592
MSBB brain gene expressionMSBBExpression4 brain regions—StagedControlledsyn69670592
MSBB brain gene expression QTLMSBBeQTL4 brain regions—StagedControlledsyn69670592
MSBB brain methylationMSBBMethylationbrain—StagedControlledsyn69670592
MSBB brain methylation QTLMSBBmQTLbrain—StagedControlledsyn69670592
MSBB brain proteomicsMSBBProteomicsbrain—StagedControlledsyn69670592
MSBB brain proteomics QTLMSBBpQTLbrain—StagedControlledsyn69670592
MSBB WGS dataMSBBGenotype / WGSblood—StagedControlled—
Non-Hispanic White Linkage Disequilibrium Reference PanelADSPLD panel16,571StagedControlledsyn53171227
ROSMAP AC alternative splicingROSMAPSplicingAC—StagedControlledsyn3388564
ROSMAP AC alternative splicing QTLROSMAPsQTLAC—StagedControlledsyn69670592
ROSMAP AC gene expressionROSMAPExpressionAC—StagedControlledsyn3388564
ROSMAP AC gene expression QTLROSMAPeQTLAC—StagedControlledsyn69670592
ROSMAP Covariates dataROSMAPCovariates—StagedControlled—
ROSMAP CUIMC1 snRNA-seq expressionROSMAPsnRNA-seqDLPFC424StagedControlledsyn31512863
ROSMAP DLPFC alternative splicingROSMAPSplicingDLPFC1,141StagedControlledsyn3388564
ROSMAP DLPFC alternative splicing QTLROSMAPsQTLDLPFC839StagedControlledsyn69670592
ROSMAP DLPFC Brain Metabolomics QTLROSMAPmetQTLDLPFC—StagedControlledsyn69670592
ROSMAP DLPFC gene expressionROSMAPExpressionDLPFC—StagedControlledsyn3388564
ROSMAP DLPFC gene expression QTLROSMAPeQTLDLPFC839StagedControlledsyn69670592
ROSMAP DLPFC GlycoproteomicsROSMAPGlycoproteomicsDLPFC—StagedControlledsyn17015098
ROSMAP DLPFC glycoproteomics QTLROSMAPglycoQTLDLPFC—StagedControlledsyn69865744
ROSMAP DLPFC H3K9acROSMAPHistone ChIP-seqDLPFC669StagedControlledsyn4896408
ROSMAP DLPFC H3K9ac QTLROSMAPhaQTLDLPFC596StagedControlledsyn69670592
ROSMAP DLPFC MetabolomicsROSMAPMetabolomicsDLPFC—StagedControlledsyn69670592
ROSMAP DLPFC methylationROSMAPMethylationDLPFC—StagedControlledsyn3157275
ROSMAP DLPFC methylation QTLROSMAPmQTLDLPFC—StagedControlledsyn69670592
ROSMAP DLPFC protein expressionROSMAPProteomicsDLPFC596StagedControlledsyn17015098
ROSMAP DLPFC protein expression QTLROSMAPpQTLDLPFC416StagedControlledsyn69670592
ROSMAP Mega snRNA-seq expressionROSMAPsnRNA-seqDLPFC—StagedControlledsyn31512863
ROSMAP MIT snRNA-seq expressionROSMAPsnRNA-seqDLPFC427StagedControlledsyn52293417
ROSMAP PCC alternative splicingROSMAPSplicingPCC—StagedControlledsyn3157322
ROSMAP PCC alternative splicing QTLROSMAPsQTLPCC—StagedControlledsyn69670592
ROSMAP PCC Expression QTLROSMAPeQTLPCC—StagedControlledsyn69670592
ROSMAP PCC gene expressionROSMAPExpressionPCC—StagedControlledsyn3157322
ROSMAP RNA-seq microglia gene expressionROSMAPExpressionmicroglia—StagedControlledsyn2580853
ROSMAP RNA-seq microglia gene expression QTLROSMAPeQTLmicroglia—StagedControlledsyn2580853
ROSMAP RNA-seq monocyte gene expressionROSMAPExpressionmonocyte—StagedControlledsyn22024496
ROSMAP RNA-seq monocyte QTLROSMAPeQTLmonocyte—StagedControlledsyn22024496
ROSMAP Single-Nucleus Alternative Splicing QTL (snSplicing)ROSMAPsQTLDLPFC, 7 cell types530StagedControlledsyn69670592
ROSMAP Single-Nucleus Chromatin Accessibility QTL (caQTL)ROSMAPcaQTLDLPFC, 6 cell types—StagedControlledsyn69670592
ROSMAP snATAC-seq Chromatin AccessibilityROSMAPsnATAC-seqDLPFC, 6 cell types—StagedControlledsyn69670592
ROSMAP snRNA-seq pseudo-bulk gene expressionROSMAPExpressionDLPFC, 7 cell types—StagedControlledsyn31512863
ROSMAP snRNA-seq pseudo-bulk gene expression QTLROSMAPsnuc-eQTLDLPFC, 7 cell types424StagedControlledsyn69670592
ROSMAP snRNA-seq Splicing (ISSAC)ROSMAPSplicingDLPFC, 7 cell types530StagedControlledsyn31512863
ROSMAP WGS dataROSMAPGenotype / WGSblood, brain—StagedControlled—
STARNET genotype dataSTARNETGenotype / WGSblood—StagedControlled—
STARNET macrophage gene expression QTLSTARNETExpressionmacrophage479StagedControlledsyn69670592
STARNET macrophage gene expression QTLSTARNETeQTLmacrophage471StagedControlledsyn69670592

N is the sample size recorded on the dataset page; — means the page does not record one. The access label describes the AD Knowledge Portal copy; "+ NG00184 open" marks results that are also open on NIAGADS DSS. Study cohorts are described on their own pages.

Full list with descriptions and lead analysts
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  • FunGen-xQTL protocol data. A toy data-set consisting of 49 de-identified samples from ROSMAP project, used to illustrates the computational protocols we developed for the detection and analysis of molecular QTLs (xQTLs).
    • Lead analysts: Hao Sun.

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  • ROSMAP AC alternative splicing. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC alternative splicing.
    • Lead analysts: Frank Grenn.
  • ROSMAP AC alternative splicing QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC alternative splicing.
    • Lead analysts: Ru Feng.
  • ROSMAP AC gene expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC gene expression.
    • Lead analysts: Frank Grenn.
  • ROSMAP AC gene expression QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC gene expression.
    • Lead analysts: Frank Grenn.
  • ROSMAP Covariates data. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) covariates data.
    • Lead analysts: There are couple of versions of covariates files been used for QTL calling, which may lead to inconsistency of data production and downstream integration analysis.
  • ROSMAP CUIMC1 snRNA-seq expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) single-nucleus RNA-seq expression data from Columbia University Irving Medical Center (CUIMC).
    • Lead analysts: Anjing Liu.
  • ROSMAP DLPFC alternative splicing. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC alternative splicing.
    • Lead analysts: Xuanhe Chen, Shrishtee Kandoi.
  • ROSMAP DLPFC alternative splicing QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC alternative splicing.
    • Lead analysts: Shrishtee Kandoi, Xuanhe Chen.
  • ROSMAP DLPFC Brain Metabolomics QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) brain tissue metabolomics QTL analysis.
    • Lead analysts: FunGen-xQTL Analysis Team.
  • ROSMAP DLPFC gene expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC gene expression.
    • Lead analysts: Xuanhe Chen.
  • ROSMAP DLPFC gene expression QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC gene expression.
    • Lead analysts: Shrishtee Kandoi, Frank Grenn.
  • ROSMAP DLPFC Glycoproteomics. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC glycoproteomics (N-glycosylation proteomics).
    • Lead analysts: FunGen-xQTL Analysis Working Group.
  • ROSMAP DLPFC glycoproteomics QTL. This page documents the glycoproteomics QTL (glycoQTL) analysis of dorsolateral prefrontal cortex (DLPFC) tissue from the Religious Orders Study (ROS) and the Rush Memory and Aging Project (MAP).
    • Lead analysts: FunGen-xQTL Analysis Working Group.
  • ROSMAP DLPFC H3K9ac. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) h3k9ac data-set.
    • Lead analysts: Xuanhe Chen, Hao Sun, Hans Klein.
  • ROSMAP DLPFC H3K9ac QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) h3k9ac QTL analysis using the FGC xQTL pipeline.
    • Lead analysts: Xuanhe Chen.
  • ROSMAP DLPFC Metabolomics.
    • Lead analysts: Brain metabolomics data from the Religious Orders Study and Memory and Aging Project (ROSMAP), profiling ~600 metabolites in dorsolateral prefrontal cortex (DLPFC) samples.
  • ROSMAP DLPFC methylation. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC methylation data-set.
    • Lead analysts: Alexandre Pelletier, Jiajun Tao.
  • ROSMAP DLPFC methylation QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC methylation data-set.
    • Lead analysts: Alexandre Pelletier.
  • ROSMAP DLPFC protein expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC protein expression.
    • Lead analysts: Zining Qi.
  • ROSMAP DLPFC protein expression QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC protein expression.
    • Lead analysts: Zining Qi.
  • ROSMAP Mega snRNA-seq expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) mega-analysis combining single-nucleus RNA-seq data from CUIMC1 and MIT.
    • Lead analysts: Anjing Liu.
  • ROSMAP MIT snRNA-seq expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) single-nucleus RNA-seq expression data from Massachusetts Institute of Technology (MIT).
    • Lead analysts: Anjing Liu.
  • ROSMAP PCC alternative splicing. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.
    • Lead analysts: Frank Grenn.
  • ROSMAP PCC alternative splicing QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.
    • Lead analysts: Frank Grenn.
  • ROSMAP PCC Expression QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.
    • Lead analysts: Frank Grenn.
  • ROSMAP PCC gene expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.
    • Lead analysts: Frank Grenn.
  • ROSMAP RNA-seq microglia gene expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) microglia data-set.
    • Lead analysts: Travyse Edwards.
  • ROSMAP RNA-seq microglia gene expression QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) microglia data-set.
    • Lead analysts: Travyse Edwards.
  • ROSMAP RNA-seq monocyte gene expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) monocyte data-set.
    • Lead analysts: Travyse Edwards.
  • ROSMAP RNA-seq monocyte QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) monocyte data-set.
    • Lead analysts: Travyse Edwards.
  • ROSMAP Single-Nucleus Alternative Splicing QTL (snSplicing). Single-nucleus alternative splicing QTL analysis from CUIMC1 & MIT harmonized snRNA-seq / Multiome data across seven major cell types.
    • Lead analysts: FunGen-xQTL Analysis Team.
  • ROSMAP Single-Nucleus Chromatin Accessibility QTL (caQTL). Single-nucleus ATAC-seq chromatin accessibility QTL analysis from ROSMAP donors, using the MIT snATAC-seq dataset described in Xiong et al., Cell 186, 4422–4437 (2023).
    • Lead analysts: FunGen-xQTL Analysis Team.
  • ROSMAP snATAC-seq Chromatin Accessibility. Single-nucleus ATAC-seq (snATAC-seq) data from ROSMAP, profiling chromatin accessibility in individual nuclei from DLPFC brain tissue.
    • Lead analysts: Anjing Liu.
  • ROSMAP snRNA-seq pseudo-bulk gene expression. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) snRNA-seq from different cells in Dorsolateral Prefrontal Cortex (DLPFC).
    • Lead analysts: Hao Sun, Masashi Fujita.
  • ROSMAP snRNA-seq pseudo-bulk gene expression QTL. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) snRNA-seq from different cells in Dorsolateral Prefrontal Cortex (DLPFC).
    • Lead analysts: Hao Sun, Masashi Fujita.
  • ROSMAP snRNA-seq Splicing (ISSAC). Single-nucleus RNA-seq splicing QTL analysis using the ISSAC (Integrative Single-cell Splicing Analysis with Context) method, applied to harmonized CUIMC1 and MIT single-nucleus data from ROSMAP DLPFC.
    • Lead analysts: Yuntian Zhang.
  • ROSMAP study info. The Religious Orders Study (ROS) and the Rush Memory and Aging Project (MAP) are two longitudinal clinical-pathologic cohort studies of aging and Alzheimer’s disease (AD), both run from Rush University.
    • Lead analysts: Xuanhe Chen.
  • ROSMAP WGS data. Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) whole-genome sequence data.
    • Lead analysts: Hao Sun, Xuanhe Chen.

S

  • STARNET genotype data. STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD).
    • Lead analysts: Travyse Edwards.
  • STARNET macrophage gene expression QTL. STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD).
    • Lead analysts: Travyse Edwards.
  • STARNET macrophage gene expression QTL (STARNET_macrophage_qtl). STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD).
    • Lead analysts: Travyse Edwards.
  • STARNET study info. STARNET is a study of RNA expression in disease-relevant tissues from living patients with cardiovascular disease (CVD).
    • Lead analysts: Travyse Edwards.

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